21ENGBIO Engineering Human Artificial Chromosomes (HACs) to Encode Genome Complexity

A hallmark of many cancers is the presence of mutations in a person's genome, for example, where some of the 23 pairs of chromosomes have either lost or gained genetic material. Prostate cancer is the most commonly diagnosed cancer in the UK and Europe, and responsible for close to 110,000 male deaths annually (IARC, 2020). Up to 20% of prostate cancer cases present hallmarks of genomic instability due to mutations in the right arm of chromosome 8, which is associated with poor survival. We believe that extra genes may be driving prostate cancer, however, there are currently no models to define these relationships and their consequences in human cells culture.
Synthetic Genomics is a bio-engineering field that uses genetic engineering and novel approaches to tackle the limitations of current methods in creating artificial DNA up to whole genome size. Synthetic Genomics enables the generation and editing of entire Human Artificial Chromosomes. By synthesising a similar length of a part of a human chromosome, but vary the order and number of the genes within the synthesized unit, the effect of gene number, location and translation can be studied. Success in this project would lead to a step-change for cell biology and the making and use of models to study human disease. This would include new models for cancer research (the exemplar used for this application).

Chromosomal instability constituting gains and losses of chromosomes is a hallmark of cancer. Gains of parts of a chromosome commonly occur: an exemplar being an 8q gain which contains close to 60 genes, including the c-Myc oncogene, observed in subsets of prostate, breast and ovarian cancer. This chromosomal gain containing many genes in a specific order is associated with these cancer's progression, treatment resistance and metastasis - yet mechanism is poorly understood.
Currently, there are no models that can recapitulate the complex condition of the gain of part of a chromosome, preventing the development of effective therapies for these cancers. Non-repetitive Human Artificial Chromosomes (HACs) could become a 'CRISPR-Cas'- equivalent: An analogous system for genomic scale engineering, permitting the design of gained loci and augmenting drug discovery. In this application, our multi- and transdisciplinary team will derive primary human prostate epithelial cultures that have been transfected with HACs that represent synthetically-engineered 8q chromosomal domains and test whether this innovative approach to genetic manipulation can lead to transcription and translation of exogenous genes with phenotypic consequence.
We argue that success in this project will support future developments in synthetic genomics platforms that combine bio-engineering, computing and robotics, to scale up the production of automated genome assembly and the re-programming of complex structures such as HACs across different cell types in human disease.